The French leader this month declared war on "Islamist separatism", which he believes is taking over some Muslim communities in France.
The Sun newspaper alleged that Pogba, a practising Muslim, reacted to Macron's comments by quitting the national team.
"Unacceptable," the 27-year-old wrote on a Twitter post along with a "fake news" sticker on a screenshot of the headline from The Sun.
The report came days after Macron paid tribute to a French history teacher who was beheaded by an Islamist radical for using cartoons of the Prophet Mohammad in a class on freedom of expression for 13-year-olds.
(Reporting by Rohith Nair in Bengaluru; Editing by Christian Radnedge)